Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy
Identifieur interne : 000131 ( Istex/Corpus ); précédent : 000130; suivant : 000132Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy
Auteurs : Lydie Grajcar ; Chahrazade El Amri ; Mahmoud Ghomi ; Serge Fermandjian ; Valerie Huteau ; Richard Mandel ; Sophie Lecomte ; Marie-Hélène BaronSource :
- Biopolymers [ 0006-3525 ] ; 2006-05.
English descriptors
- Teeft :
- Accessibility, Adenine, Adenyl, Adenyl residue activity assessment, Adenyl residues, Average base, Base pairing, Base residues, Biochem, Biochemistry, Biol, Biomol struct, Biophys, Biopolymers, Chem, Colloid, Corresponding duplexes, Curr, Curr opin struct biol, Docking, Duplex, Electropositive, Electropositive domains, Electropositive sites, Exibility, Exible, Gaaa, Gaga, Gcaa, Ggaa, Ggga, Gnra, Gnra loops, Grajcar, Great variety, Guaa, Hairpin, Hairpin stability, Hairpin structure, Hairpin structures, High dilution, High ratio, Hyperchromicity, Ipping, Less reactive, Locus, Loop, Lower concentration, Mgcl2, Mgcl2 medium, Mismatch, Mispairing, Moiety, More reactive, Nacl, Nacl medium, Nucleic, Nucleic acid, Nucleic acids, Nucleic bases, Nucleotide, Oligomers, Opin, Pairing, Palindromic, Plasmon, Plasmon spectra, Polymer, Proc natl acad, Racc, Raman, Raman spectrosc, Reactive, Reactivity, Residue, Rgnra loops, Same concentration, Secondary structures, Sers, Silver aggregates, Silver particles, Silver plasmon spectra, Steric hindrance, Struct, Structural stability, Studies show, Triloops, Universite paris, Water molecules.
Abstract
We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl− and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n ≫ (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self‐association and duplex structures. In d hairpins the solvent‐exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent‐exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross‐bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross‐bridging enables “A flipping” much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6–28, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Url:
DOI: 10.1002/bip.20455
Links to Exploration step
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<term>Adenyl residue activity assessment</term>
<term>Adenyl residues</term>
<term>Average base</term>
<term>Base pairing</term>
<term>Base residues</term>
<term>Biochem</term>
<term>Biochemistry</term>
<term>Biol</term>
<term>Biomol struct</term>
<term>Biophys</term>
<term>Biopolymers</term>
<term>Chem</term>
<term>Colloid</term>
<term>Corresponding duplexes</term>
<term>Curr</term>
<term>Curr opin struct biol</term>
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<term>Duplex</term>
<term>Electropositive</term>
<term>Electropositive domains</term>
<term>Electropositive sites</term>
<term>Exibility</term>
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<term>Grajcar</term>
<term>Great variety</term>
<term>Guaa</term>
<term>Hairpin</term>
<term>Hairpin stability</term>
<term>Hairpin structure</term>
<term>Hairpin structures</term>
<term>High dilution</term>
<term>High ratio</term>
<term>Hyperchromicity</term>
<term>Ipping</term>
<term>Less reactive</term>
<term>Locus</term>
<term>Loop</term>
<term>Lower concentration</term>
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<term>More reactive</term>
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<term>Nucleic acid</term>
<term>Nucleic acids</term>
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<front><div type="abstract" xml:lang="en">We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl− and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n ≫ (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self‐association and duplex structures. In d hairpins the solvent‐exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent‐exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross‐bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross‐bridging enables “A flipping” much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6–28, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com</div>
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<p>We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]<formula><math><msubsup><mtext> </mtext>
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binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6–28, 2006</p>
<p>This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com</p>
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<affiliation xml:id="af5" countryCode="FR" type="organization"><unparsedAffiliation>Institut Pasteur, Unité de Chimie Organique, 28 rue de Docteur Roux, 75724, Paris, France</unparsedAffiliation>
</affiliation>
<affiliation xml:id="af6" countryCode="US" type="organization"><unparsedAffiliation>Department of Pathology, Boston University School of Medicine, Boston, MA 022118, USA</unparsedAffiliation>
</affiliation>
</affiliationGroup>
<keywordGroup xml:lang="en" type="author"><keyword xml:id="kwd1">adenyl reactivity</keyword>
<keyword xml:id="kwd2">nucleic acids</keyword>
<keyword xml:id="kwd3">magnesium</keyword>
<keyword xml:id="kwd4">SERS</keyword>
</keywordGroup>
<abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title>
<p>We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]<math altimg="urn:x-wiley:00063525:media:BIP20455:tex2gif-stack-1" wiley:location="equation/tex2gif-stack-1.gif"><msubsup><mtext> </mtext>
<mrow><mtext fontstyle="italic">n</mtext>
</mrow>
<mrow><mtext>+</mtext>
</mrow>
</msubsup>
</math>
sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl<sup>−</sup>
and Na<sup>+</sup>
or Mg<sup>2+</sup>
ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (<i>r</i>
) than in deoxyribo (<i>d</i>
) species [pA > p<i>d</i>
A and (pA)<sub><i>n</i>
</sub>
≫ (p<i>d</i>
A)<sub><i>n</i>
</sub>
]. Base pairing decreases A reactivity in corresponding duplexes but much less in <i>r</i>
than in <i>d</i>
. In linear single and paired <i>d</i>
CAG or <i>d</i>
GAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A<sup>.</sup>
A). <i>d</i>
A tracts are highly reactive only when dilution prevents self‐association and duplex structures. In <i>d</i>
hairpins the solvent‐exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight <i>r</i>
G<sup>1</sup>
N<sup>2</sup>
R<sup>3</sup>
A<sup>4</sup>
loops, those bearing a single A (A<sup>4</sup>
) are the least reactive. The solvent‐exposed A<sup>2</sup>
is reactive, but synergistic structural transitions make the initially stacked A residues of any <i>r</i>
GNAA loop much more reactive. Mg<sup>2+</sup>
cross‐bridging single strands via phosphates may screen A reactivity. In contrast <i>d</i>
duplexes cross‐bridging enables “A flipping” much more in <i>r</i>
A<sup>.</sup>
U pairs than in <i>d</i>
A<sup>.</sup>
T. Mg<sup>2+</sup>
promotes A reactivity in unpaired strands. For hairpins Mg<sup>2+</sup>
binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6–28, 2006</p>
<p>This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com</p>
</abstract>
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<mods version="3.6"><titleInfo lang="en"><title>Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy</title>
</titleInfo>
<titleInfo type="abbreviated" lang="en"><title>Adenyl Residue Activity Assessment</title>
</titleInfo>
<titleInfo type="alternative" contentType="CDATA" lang="en"><title>Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy</title>
</titleInfo>
<name type="personal"><namePart type="given">Lydie</namePart>
<namePart type="family">Grajcar</namePart>
<affiliation>Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Chahrazade</namePart>
<namePart type="family">El Amri</namePart>
<affiliation>Laboratoire Protéines, Biochimie Structurale et Fonctionnelle, FRE 2852, Université Paris 6, Tour Jacques Monod, 4 place Jussieu, 75005, Paris,Cedex 05, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Mahmoud</namePart>
<namePart type="family">Ghomi</namePart>
<affiliation>Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, Université Paris 6, Génopole Campus 1, Site Serano‐RN75, 91030, Evry, Cedex, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Serge</namePart>
<namePart type="family">Fermandjian</namePart>
<affiliation>Département de Biologie et Pharmacologie Structurale, UMR 8113 CNRS, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805, Villejuif et ENS‐Cachan,61 Avenue du Président Wilson 94235, Cachan, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Valerie</namePart>
<namePart type="family">Huteau</namePart>
<affiliation>Institut Pasteur, Unité de Chimie Organique, 28 rue de Docteur Roux, 75724, Paris, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Richard</namePart>
<namePart type="family">Mandel</namePart>
<affiliation>Department of Pathology, Boston University School of Medicine, Boston, MA 022118, USA</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Sophie</namePart>
<namePart type="family">Lecomte</namePart>
<affiliation>Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France</affiliation>
<affiliation>E-mail: sophie.lecomte@glvt‐cnrs.fr</affiliation>
<affiliation>Correspondence address: Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">Marie‐Hélène</namePart>
<namePart type="family">Baron</namePart>
<affiliation>Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
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<abstract lang="en">We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl− and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n ≫ (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self‐association and duplex structures. In d hairpins the solvent‐exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent‐exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross‐bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross‐bridging enables “A flipping” much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6–28, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com</abstract>
<subject lang="en"><genre>keywords</genre>
<topic>adenyl reactivity</topic>
<topic>nucleic acids</topic>
<topic>magnesium</topic>
<topic>SERS</topic>
</subject>
<relatedItem type="host"><titleInfo><title>Biopolymers</title>
<subTitle>Original Research on Biomolecules</subTitle>
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<titleInfo type="abbreviated"><title>Biopolymers</title>
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<subject><genre>article-category</genre>
<topic>Regular Article</topic>
<topic>Regular Articles</topic>
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<identifier type="ISSN">0006-3525</identifier>
<identifier type="eISSN">1097-0282</identifier>
<identifier type="DOI">10.1002/(ISSN)1097-0282</identifier>
<identifier type="PublisherID">BIP</identifier>
<part><date>2006</date>
<detail type="volume"><caption>vol.</caption>
<number>82</number>
</detail>
<detail type="issue"><caption>no.</caption>
<number>1</number>
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